OrthoDB8 clustering and mapping of i5K species

PRIVATE DATA: please contact i5K project leaders for usage permissions.
Please contact Evgeny Zdobnov with any questions (Evgeny dot Zdobnov at unige dot ch)


10 i5K species included in OrthoDB8 clustering
18 i5K species later mapped to OrthoDB8
Many other arthropods from OrthoDB8
Selected outgroup species from OrthoDB8

Orthologous groups
Group ID and Gene ID text files for all species and all major radiations of the phylogeny  
Metazoa, Arthropoda, Insecta, Endopterygota, Diptera, Lepidoptera, Coleoptera, Hymenoptera, etc.

Phylogenomics and Gene Families
Phylogenies of the major radiations with ultrametric trees and gene family evolution etc. View
Significantly different median gene counts per lineage View

Protein Alignment Data

1. Pairwise alignments: for each pair of species ::: SpeciesA_SpeciesB.align

2. Best-Reciprocal-Hits: for each pair of species ::: SpeciesA_SpeciesB.brh

Columns in .align and .brh files = protein_id1 protein_id2 score evalue percent_identity start1 end1 start2 end2

3. ID maps: OrthoDB protein ID to public protein ID mapping ::: SPECIES.idmap.txt

4. 97% paralogs: near-identical proteins from each species are identified before clustering/mapping
One representative (longest) is chosen for clustering/mapping, then its paralogs are added at the end
SPECIES.97pc.txt files give the representative protein ID followed by a comma-seperated list of its paralogs

# OrderCodeTaxonIDSpecies & NameMapped/Clustered
8 Arachnida CSCUL 218467Centruroides sculpturatus Bark scorpionMAPPED
ISCAP 6945Ixodes scapularis Black-legged deer tickCLUSTERED
LHESP 256737Latrodectus hesperus Western black widow spiderMAPPED
LRECL 6921Loxosceles reclusa Brown recluse spiderMAPPED
MOCCI 34638Metaseiulus occidentalis Western predatory miteCLUSTERED
PTEPI 114398Parasteatoda tepidariorum Common house spiderMAPPED
SMIMO 407821Stegodyphus mimosarum African social velvet spiderCLUSTERED
TURTI 32264Tetranychus urticae Two-spotted spider miteCLUSTERED
1 Blattodea BGERM 6973Blattella germanica German cockroachMAPPED
6 Coleoptera AGLAB 217634Anoplophora glabripennis Asian longhorned beetleCLUSTERED
APLAN 224129Agrilus planipennis Emerald ash borerMAPPED
DPOND 77166Dendroctonus ponderosae Mountain pine beetleCLUSTERED
LDECE 7539Leptinotarsa decemlineata Colorado potato beetleCLUSTERED
OTAUR 166361Onthophagus taurus Bull-headed dung beetleMAPPED
TCAST 7070Tribolium castaneum Red flour beetleCLUSTERED
3 Crustacea DPULE 6669Daphnia pulex Water fleaCLUSTERED
EAFFI 88015Eurytemora affinis Calanoid copepodMAPPED
HAZTE 294128Hyalella azteca Freshwater epibenthic amphipodMAPPED
1 Diplura CAQUI 438503Catajapyx aquilonaris Silvestris Northern ForcepstailMAPPED
14 Diptera AAEGY 7159Aedes aegypti Yellowfever mosquitoCLUSTERED
AALBI 7167Anopheles albimanus New World malaria mosquitoCLUSTERED
AFUNE 62324Anopheles funestus African malaria mosquitoCLUSTERED
AGAMB 7165Anopheles gambiae African malaria mosquitoCLUSTERED
CCAPI 7213Ceratitis capitata Mediterranean fruit flyCLUSTERED
CQUIN 7176Culex quinquefasciatus Southern house mosquitoCLUSTERED
DGRIM 7222Drosophila grimshawi Fruit flyCLUSTERED
DMELA 7227Drosophila melanogaster Fruit flyCLUSTERED
DPSEU 7237Drosophila pseudoobscura Fruit flyCLUSTERED
GMORS 7394Glossina morsitans Savannah tsetse flyCLUSTERED
LCUP2 7375Lucilia cuprina Sheep blowflyMAPPED
LLONG 7200Lutzomyia longipalpis Sand FlyCLUSTERED
MDEST 39758Mayetiola destructor Hessian flyCLUSTERED
MDOME 7370Musca domestica House flyCLUSTERED
1 Ephemeroptera EDANI 1049336Ephemera danica Green drake mayflyCLUSTERED
7 Hemiptera APISU 7029Acyrthosiphon pisum Pea aphidCLUSTERED
CLECT 79782Cimex lectularius Bed bugCLUSTERED
GBUEN 56086Gerris buenoi Water striderMAPPED
HHALY 286706Halyomorpha halys Brown marmorated stink bugMAPPED
HVITR 197043Homalodisca vitripennis Glassy winged sharpshooterMAPPED
OFAS2 77536Oncopeltus fasciatus Milkweed bugMAPPED
PVENU 38123Pachypsylla venusta Hackberry petiole gall psyllidMAPPED
24 Hymenoptera ACEPH 12957Atta cephalotes Leafcutter antCLUSTERED
AECHI 103372Acromyrmex echinatior Panamanian leafcutter antCLUSTERED
AFLOR 7463Apis florea Little honey beeCLUSTERED
AMELL 7460Apis mellifera Honey beeCLUSTERED
AROSA 37344Athalia rosae Turnip sawflyCLUSTERED
BIMPA 132113Bombus impatiens Common eastern bumble beeCLUSTERED
BTERR 30195Bombus terrestris Buff-tailed bumble beeCLUSTERED
CCINC 211228Cephus cinctus Wheat stem sawflyCLUSTERED
CFLOR 104421Camponotus floridanus Florida carpenter antCLUSTERED
COBSC 286306Cardiocondyla obscurior Tramp antCLUSTERED
COPFL 29053Copidosoma floridanum WaspMAPPED
DNOVA 178035Dufourea novaeangliae Solitary univoltine beeCLUSTERED
EMEXI 516756Eufriesea mexicana Orchid beeCLUSTERED
HLABO 597456Habropoda laboriosa Southeastern blueberry beeCLUSTERED
HSALT 610380Harpegnathos saltator Jerdons jumping antCLUSTERED
LALBI 88501Lasioglossum albipes Halictid beeCLUSTERED
LHUMI 83485Linepithema humile Argentine antCLUSTERED
MQUAD 166423Melipona quadrifasciata Neotropical stingless beeCLUSTERED
MROTU 143995Megachile rotundata Alfalfa leafcutting beeCLUSTERED
NVITR 7425Nasonia vitripennis Parasitic jewel waspCLUSTERED
OABIE 222816Orussus abietinus Parasitic wood waspCLUSTERED
PBARB 144034Pogonomyrmex barbatus Red harvester antCLUSTERED
SINVI 13686Solenopsis invicta Red fire antCLUSTERED
TPRET 7493Trichogramma pretiosum Parasitic stingless waspCLUSTERED
1 Isoptera ZNEVA 136037Zootermopsis nevadensis Dampwood termiteCLUSTERED
5 Lepidoptera BMORI 7091Bombyx mori Domestic silkworm mothCLUSTERED
DPLEX 13037Danaus plexippus Monarch butterflyCLUSTERED
HMELP 34740Heliconius melpomene Postman butterflyCLUSTERED
MSEXT 7130Manduca sexta Tobacco hornworm mothCLUSTERED
PXYLO 51655Plutella xylostella Diamondback mothCLUSTERED
1 Myriapoda SMARI 126957Strigamia maritima Geophilimorph centipedeCLUSTERED
1 Odonata LFULV 123851Ladona fulva Scarce chaser dragonflyCLUSTERED
13 Outgroups BTAUR 9913Bos taurus CattleCLUSTERED
CELEG 6239Caenorhabditis elegans Nematode wormCLUSTERED
CINTE 7719Ciona intestinalis Vase tunicate sea squirtCLUSTERED
CTELE 283909Capitella teleta Polychaete annelid wormCLUSTERED
DRERI 7955Danio rerio ZebrafishCLUSTERED
GGALL 9031Gallus gallus ChickenCLUSTERED
HSAPI 9606Homo sapiens HumanCLUSTERED
LGIGA 225164Lottia gigantea Owl limpet molluscCLUSTERED
MMUSC 10090Mus musculus House mouseCLUSTERED
NVECT 45351Nematostella vectensis Starlet sea anemoneCLUSTERED
OANAT 9258Ornithorhynchus anatinus Duckbill platypusCLUSTERED
SPURP 7668Strongylocentrotus purpuratus Purple sea urchinCLUSTERED
XTROP 8364Xenopus tropicalis Western clawed frogCLUSTERED
1 Phthiraptera PHUMA 121225Pediculus humanus Body louseCLUSTERED
1 Thysanoptera FOCCI 133901Frankliniella occidentalis Western flower thripCLUSTERED
1 Trichoptera LLUNA 1218281Limnephilus lunatus CaddisflyMAPPED

        LINKS: Zdobnov's Computational Evolutionary Genomics Group CEGG and the Hierarchical Catalog of Orthologs OrthoDB